Workflow

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Duplicate explicit target name: "multiqc_report.html".

Detailed software versions can be found under Rules

Results

Quality control

multiqc_report.html

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multiqc_report.html

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Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Rules

Rule Jobs Output Singularity Conda environment
bwa_index 2
  • data/GCA_002873125.1_ASM287312v1_genomic.fna.amb
  • data/GCA_002873125.1_ASM287312v1_genomic.fna
  • data/GCA_002873275.1_ASM287327v1_genomic.fna.amb
  • data/GCA_002873275.1_ASM287327v1_genomic.fna
multiqc_raw 1
  • analysis/fastqc_raw/multiqc_report.html
freebayes 2
  • analysis/freebayes/12NC29_all.vcf
  • analysis/freebayes/12SD80_all.vcf
index 2
  • data/GCA_002873125.1_ASM287312v1_genomic.fna.fai
  • data/GCA_002873275.1_ASM287327v1_genomic.fna.fai
multiqc_trim 1
  • analysis/fastqc_trimmed/multiqc_report.html
fastqc_raw 4
  • analysis/fastqc_raw/15FL1-2_R1.small_fastqc.zip
  • analysis/fastqc_raw/15Fl1-4_R1.small_fastqc.zip
  • analysis/fastqc_raw/15Fl1-4_R2.small_fastqc.zip
  • analysis/fastqc_raw/15FL1-2_R2.small_fastqc.zip
markdup 4
  • analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG_mdup.bam
  • analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG_mdup.bam
  • analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG_mdup.bam
  • analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG_mdup.bam
fastqc_trim 4
  • analysis/fastqc_trimmed/15Fl1-4_R2_trim_fastqc.zip
  • analysis/fastqc_trimmed/15FL1-2_R2_trim_fastqc.zip
  • analysis/fastqc_trimmed/15Fl1-4_R1_trim_fastqc.zip
  • analysis/fastqc_trimmed/15FL1-2_R1_trim_fastqc.zip
bam_sort 4
  • analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG_sorted.bam
  • analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG_sorted.bam
  • analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG_sorted.bam
  • analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG_sorted.bam
trimmomatic 2
  • analysis/trimmed/15Fl1-4_R1_trim.fastq.gz
  • analysis/trimmed/15Fl1-4_R2_trim.fastq.gz
  • analysis/trimmed/15Fl1-4_R1_trim.unpaired.fastq.gz
  • analysis/trimmed/15Fl1-4_R2_trim.unpaired.fastq.gz
  • analysis/trimmed/15FL1-2_R1_trim.fastq.gz
  • analysis/trimmed/15FL1-2_R2_trim.fastq.gz
  • analysis/trimmed/15FL1-2_R1_trim.unpaired.fastq.gz
  • analysis/trimmed/15FL1-2_R2_trim.unpaired.fastq.gz
read_groups 4
  • analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ_RG.bam
  • analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ_RG.bam
  • analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ_RG.bam
  • analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ_RG.bam
map_filter 4
  • analysis/bwa_filtered/12NC29/15FL1-2_30MAPQ.bam
  • analysis/bwa_filtered/12NC29/15Fl1-4_30MAPQ.bam
  • analysis/bwa_filtered/12SD80/15FL1-2_30MAPQ.bam
  • analysis/bwa_filtered/12SD80/15Fl1-4_30MAPQ.bam
sam_to_bam 4
  • analysis/bwa/12NC29/15FL1-2.bam
  • analysis/bwa/12NC29/15Fl1-4.bam
  • analysis/bwa/12SD80/15FL1-2.bam
  • analysis/bwa/12SD80/15Fl1-4.bam
bwa_mem 4
  • analysis/bwa/12NC29/15FL1-2.sam
  • analysis/bwa/12NC29/15Fl1-4.sam
  • analysis/bwa/12SD80/15FL1-2.sam
  • analysis/bwa/12SD80/15Fl1-4.sam